Charlie Morton’s three-year contract extension stands as the team’s biggest move. Pitcher Edinson Volquez is the team’s richest free agent signing of the year at $5 million. Outside of that, the Pirates have been just about dormant.

Spring training is set to begin this week, and the Bucs still have more questions than answers at several key positions.

Despite their success last season, the Pirates will again turn to unproven internal options to vie for jobs other contenders addressed in the first weeks of the offseason. While the team indeed missed out on targeted free agents who could have filled very real voids at first base and in right field, their biggest offseason question mark always remained A.J. Burnett, who became a free agent after the 2013 season.

The Burnett question has been answered — he signed with the Phillies on a one-year, $16 million deal a day before pitchers and catchers report to Pirate City for the unofficial start of Spring Training. But in true Pirates fashion, one answer leaves several questions in its wake.

Key among them — why did the Pirates allow Burnett to leave the team for nothing?

Now 37, Burnett was set to be a free agent at the end of last season. He played out the final two years of his five-year contract (signed with the Yankees) in Pittsburgh, and the Pirates got full value for him. Burnett was instrumental in turning around the clubhouse mentality of the perennial doormat Bucs, and his on-field performance was equally important, helping to lift the Pirates from 90 losses in the year before his arrival to a winning record and playoff run last season.

The Pirates declined to extend Burnett a qualifying offer before the deadline to issue QO’s passed in November, and that move has proven key to the whole Burnett saga. Qualifying offers are a way for teams to recapture some value from free agents they feel they won’t be able to re-sign. The value of those offers is based on league-average salaries and apply to one-year offers. Players who turn down their QO’s and sign with new teams cost their new team a draft pick, which the former team is awarded at the end of the first round.

It’s a move meant to help small market clubs recover lost value, but has so far pinned a number of proven players to the throes of free agency.

For 2014, the one-year QO value is set at $14.1 million. Had Burnett been tendered and signed a QO, he would have been the highest-paid player on the roster, some $1 million more than the $13 million being earned by Wandy Rodriguez this season (a portion of which is still being picked up by the Houston Astros). It would have also been the first time the Pirates paid for Burnett entirely out of pocket. The Yankees covered nearly half his salary in 2012 and 2013.

The Pirates, of course, declined to make a QO last November, but at the time the moved appeared to be a formality. Burnett publicly stated that in 2014 he would be a Pirate, or he’d be retired.

Of course, taking a player at his word is no way to build a roster on a shoestring budget.

The Pirates waited on Burnett nonetheless. The weeks turned to months and both scenarios grew increasingly unlikely. Burnett’s status seemed to hold the team’s free agent plans and a good deal of salary space in limbo all winter. Wednesday, Burnett broke his offseason gag order and signed a one-year deal with the Philadelphia Phillies worth $16 million. That deal is worth just about $2 million more than the $14.1 million QO the Pirates declined to offer him in November and $4 million more than the reported $12 million the team offered Burnett before he decided to sign with the Phillies.

It was never a guarantee that the Pirates could have re-signed Burnett. He ended up getting $16 million. He might have gotten $30 million. Baseball is weird that way, and you can’t predict the actions of ball clubs with more money than brains. No matter what Burnett chose to sign for, the Bucs at least had the option of extending him a qualifying offer.

Instead, they missed out. On everything.

The Pirates are not in a rebuild, but for a team in the bottom tier of MLB payrolls, asset management is the key to fielding a competitive roster. That means spending well, drafting well, and shrewdly acquiring the assets that are available to them.

In most cases of small market asset management, these Pirates strike gold. They’ve revived a number of fading veterans on low-rent deals and seem to build above-average bullpens out of the free agent parts bin. They’ve also drafted well under GM Neal Huntington, even as the league imposes draconian measures like draft slotting, which robs small market teams of their only apparent advantage against the league’s richer half.

However, failing to issue Burnett a qualifying offer, and subsequently failing to get a draft pick in his absence, is a major misstep.

Whether or not Burnett’s performance would have made him worthy of the team’s highest salary for a third straight year is immaterial. That $14.1 million would have been slightly under market for Burnett, as evidenced by his $16 million contract with Philadelphia. While the Pirates obviously have their own market for free agents — the uncapped MLB player’s market and hyper-spendthrift habits of Pirates owner Bob Nutting are equally at work here — $14.1 million seems more than fair for a number-two or -three starter who provided nearly 200 innings and an NL-leading 9.8 strikeouts-per-nine-innings a year ago.

“Teams that offer qualifying offers either feel very strongly that the player is going to get a multiyear deal elsewhere that incentivizes them to decline the qualifying offer, or they have complete comfort with that player returning on the fourteen-plus-million qualifying offer,” Huntington said. “In both scenarios, the answer was ‘no’ for us.”

– Neal Huntington, Pittsburgh Tribune-Review. 12 Feb 2014

The Pirates, of course, did not match the Phillies offer. Which begs the question: why lose him to another team for nothing?

The big caveat here is a detail not revealed until after Burnett’s move to Philadelphia had been finalized. At some point this offseason, the Pirates offered Burnett $12 million for a one-year deal, as first reported by Jon Heyman and later confirmed by the Pittsburgh Tribune-Review.

If the team offered him that money from the get-go, it’s very unlikely they would have declined to make him a qualifying offer. The difference between their offer and the qualifying offer was just too slim when a possible draft pick was in play. One assumes that offer came in the later stages of free agency, where the market for Burnett would have cooled and his asking price subsequently would have come down.

If that was the case, the decision to wait may not have just cost them Burnett. The Pirates, as mentioned, count every penny. If that $12 million or so was being left alone in the event of re-signing Burnett, that could have lessened the team’s other offers and hurt their chances of signing other players like James Loney, to whom the Bucs made an offer but ultimately missed out on.

The Penguins went through a similar episode in 2008, when free agent winger Marian Hossa declined to announce his intentions with the Pens are remained unsigned until two days into free agency. As a result, the Penguins lost both Hossa and other newly signed players they might have targeted with the money set aside for him. From that point on, the Penguins haven’t let a single free agent hold them hostage. To the contrary, the team has acted ahead of the market. They traded former number-two overall pick Jordan Staal in 2012 when it became clear he might not re-sign. Rather than lose him for nothing (and the NHL has no draft compensation for free agents), the Penguins got a huge return by virtue of being proactive.

These are two different leagues, obviously, but there remains a similar benefit to staying ahead of the market and not being held hostage by your players.

It was widely assumed that the Pirates could not or did not want to match the kind of money Burnett could have earned elsewhere. In markets like Pittsburgh, a million here and two million there can make a difference. But how big a difference? At worst, the Pirates came up short of Burnett’s new deal by $4 million. Had they offered Burnett a QO and the accompanying loss of a draft pick made him unsignable elsewhere (and this is a real problem with the current build of qualifying offers), the Pirates would have gotten their innings and strikeouts leader back at just $2 million more than they had hoped to sign him for.

Instead, nothing. Not the player. Not a pick. Over a difference of a few million dollars.

The Pirates, of all clubs, ought to know how valuable a draft pick can be.

According to a recent story by ESPN, the 20th overall selection in the upcoming draft is valued at some $23 million. That’s quite a lot of money for an unproven quantity. Beyond that figure, the Pirates have built the foundation of their club — their top starter, two infielders and what will eventually be the entire outfield — through the draft. After six years, the Pirates under Huntington field one of the most highly-regarded farm systems in baseball. Some of those players were traded for in salary dumps past, but most of that farm system was drafted by the Pirates’ current management team.

Pittsburgh has relied on the draft more than perhaps any team in baseball in recent years. Before MLB instituted its draft-slotting system, no team from 2007 to 2012 spent more on draft signings than the Pirates. The method worked. Pittsburgh has become a contender in the NL Central, and their deep prospect pool figures to keep them competitive even as their top prospects develop into professionals with high earning potential.

Unless there were other factors that stayed in the room which led the Pirates to passing on Burnett, their assessment of not making a qualifying offer came down to saving some $2 million. It now seems that decision will cost them what would have either been a late first-round draft pick or a veteran starter with inning-eating potential.

Those are the kinds of things the Pirates just can’t mismanage.

As for the $12 million that’s now burning a hole in the Pirates’ back pocket, it’s very hard to guess at what the finances of a ball club are really like. Unlike salary-capped leagues like the NHL, you just can’t tell where the money is going. For example, the Penguins have two free agent defensemen due for new deals at the end of this season, and a small amount of cap space with which to sign them. If one is signed and the other let go to free agency, there’s an A-to-B line that explains how available payroll plays its part in personnel decisions.

Baseball has no salary cap, but the Pirates apparently have a very strict internal idea of how the Major League payroll is to be handled. That leaves fans guessing where the $12 million not spent on Burnett is going to go.

Will the team bank it and use it in future negotiations with players like Gerrit Cole and Pedro Alvarez? They could sit on that cash and spend it at the trade deadline — many of the team’s veteran acquisitions in recent years have come not during free agency, but before the MLB Trade Deadline. That $12 million could be used to acquire a hard-hitting infielder or depth bullpen option as the team gears up for the stretch run. Or, it could be used to lavish some new accouterments on the luxury boxes at PNC Park.

Fans really never get the whole finance picture in any league, nor of any team. But the nature of the Pirates and of MLB as a whole makes the entire process clouded and, in cases similar to Burnett’s, frustrating.

The Pirates are truly building from the inside-out, and by 2014 are starting to not just collect prospects, but graduate them to the Majors. It may be the case that the money not spent on Burnett will reappear down the road to help pay for the long-term contract of a budding star.

However, that line can never be clearly drawn for fans. And since nobody but the Pirates knows how the money is being managed, the loss of Burnett and a possible draft pick is just too big an oversight to overlook.

About the Author

Writer for sale. I run Slew Footers and contribute to a few other sports blogs. Shower me with your praise and adulation on twitter @slew_james.